1
Q
what happens to nutrient molecules during reactions in cells
A
they are degraded
2
Q
what role does chemical energy play in cell reactions
A
they are conserved and transformed
3
Q
what happens to macromolecules during reactions in cells
A
they are made from simple precursors
4
Q
T/F chemical reactions must take place at a rate that meets a cells needs
A
true
5
Q
what must be specific, so a chemical reaction takes place in a cell
A
- particular reactant should always yield a specific product
- side-reactions producing useless or toxic byproducts must be minimized
- correct orientation and right amount of energy
6
Q
what role do enzymes play in cell reactions
A
reactions are accelerated and made highly specific by enzymes
- provide optimal distance and orientation
7
Q
what holds amino acid side chains that conform correct fitting in an enzyme
A
binding pockets
8
Q
where is carbonic anhydrase present
A
red blood cells
9
Q
what is the purpose of carbonic anhydrase
A
allows transport of CO2 from the tissues to the lungs where it is exhaled
10
Q
CO2 levels in the tissue
A
high CO2 -> low pH -> low O2 binding to Hb
(high acidity lowers Hb affinity)
11
Q
CO2 levels in lungs
A
low CO2 -> higher pH -> higher O2 binding to Hb
12
Q
hydrolysis site for trypsin (enzyme specificity) and where are the cut marks
A
C-terminus of Lys or Arg of base pair
- KKX
- RKX
- KRX
- RRX
13
Q
hydrolysis site for thrombin (enzyme specificity) and where are the cut marks
A
- more specific than trypsin
ARG-GLY bond cleavage in specific sequence - (Leu-Val-Pro-Arg*-Gly-Ser)
14
Q
T/F most enzymes are proteins
A
true
(except small group of catalytic RNAs: ribozymes)
15
Q
what does the catalytic activity of enzymes depend on
A
the integrity of enzymes native conformation, and appropriate conditions
(pH, temp, salts)
16
Q
T/F enzymes are present in large amoutns
A
false, very small
17
Q
T/F the activity of enzymes is always regulated
A
true
18
Q
what does the suffix of “ase” mean when added to an enzyme name
A
describes their activity
19
Q
glucokinase activity
A
phosphate added to glucose
20
Q
phosphatase activity
A
phosphate removed from glucose
21
Q
T/F most enzymes require chemical groups for activity other than their own amino acids
A
false, they do not require chemical groups
22
Q
T/F some enzymes require additional cofactors for activity
A
true
23
Q
what is the fold rate enhancement by carbonic anhydrase
A
10^7
24
Q
how does temperature influence the rate of enzyme reactions
A
- higher temp accelerates reactions by increasing KE and collision frequency of reactants in both catalyzed and uncatalyzed reactions
- too high temperature will denature an enzyme
25
how does pH influence the rate of enzyme reactions
- ionization of active site and enzyme stability
- most enzymes have characteristic pH optimum
26
what are the 4 catalytic strategies used by enzymes
- covalent catalysis
- general acid-base catalysis
- metal ion catalysis
- proximity and orientation
27
covalent catalysis
the active site contains a reactive group (nucleophile) that is briefly covalently modified
28
general acid-base catalysis
a molecule other than water donates or accepts a proton
29
metal ion catalysis
metal ions (positive charge) can function in various ways
- stabilize a negative charge on a reaction intermediate
- generate a nucleophile by deprotonating water
- bind to S, increase interactions with E, increasing binding energy
30
proximity and orientations (enzyme strategy)
enzyme brings two substrates close together and orients the reacting parts of substrate molecules for reaction
31
oxidoreductases
transfer electrons between molecules: catalyze oxidation-reduction reactions
(lose or gain electrons)
32
transferases
transfer functional groups between separate molecules
33
hydrolases
cleave molecules by the addition of water
(when water is activated, water cleaves substrate)
34
lyases
breaks bonds without hydrolysis and oxidation (difficult)
35
isomerases
move functional groups within a molecules (one carbon to another)
36
ligases
join two molecules at the expense of ATP hydrolysis (difficult)
37
what does the catalytic activity of enzymes depend on
the presence of small molecules: cofactors (coenzymes)
38
enzyme minus its cofactor
apoenzyme (not active)
39
complete catalytically active enzyme plus its cofactor
holoenzyme
40
what are the two divisions of cofactors
coenzymes
metals
41
coenzymes
small organic molecules (coenzyme A) derived from vitamins can serve as transient carriers of electrons or specific functional groups
42
coenzyme that is very tightly bound to an enzyme name
prosthetic group (heme)
43
what re examples of a coenzyme that can be used by a variety of enzymes
(NAD+, NADH)
44
T/F different enzymes that use a same cofactor usually carry out similar chemical reactions
true
45
T/F the least stable species in reaction has the highest free energy
true
46
activation energy
the difference in free energy between the transition state and the substrate
47
where does energy come from for lowering of Gibbs free energy by an enzyme
binding energy
48
active site
the pocket of an enzyme lined with aa residues that bind the substrate and catalyze its chemical transformation
49
enzyme substrate (ES) complex -> _____ activation energy
lower
50
electrostatic complementary interaction between AA side chains and substrate
good: lys+ -><- glu-
bad: arg+ <-->lys+ or glu- <--> Asp-
51
hydrophobic complementary interaction between AA side chains and substrate
good: val -><- leu
bad: Arg+ <--> val or Ser <--> Phe
52
hydrogen bond complementary interaction between AA side chains and substrate
good: Ser -><- Gli
(common for metabolism)
53
disulfide complementary interaction between AA side chains and substrate
only Cys-Cys
(SH side chain)
54
Pi-Pi complementary interaction between AA side chains and substrate
Phe/Tyr -><- Phe/Tyr
55
Pi-Cation complementary interaction between AA side chains and substrate
Phe -><- Lys/Arg
56
4 common features of active sites
- 3D cleft or crevices that provide unique environment (H2O excluded unless reactant)
- takes up a small pat of total volume of enzyme
- bind substrates, products, and transition states via multiple weak attractions
- structural complementarity (after binding)
57
lock and key model of substrate binding
substrate + active site -- enzyme = ES complex
- enzymes are flexible
- shapes of active sites are modified when S binds
- binding that is too tight makes it harder for S to reach transition state
58
induced fit model of substrate binding
E itself undergoes a change in conformation upon binding S
- permits formation of additional weak binding interactions in transition state
- brings specific functional groups into proper position for catalysis
59
binding energy of the ES complex
- many weak, non-covalent interactions
- formation of each bond is accompanied by small release of free energy, contributing to stability of interaction
- total energy derived from ES interactions = binding energy
- weak interactions optimized when S is in transition state
60
binding energy definition
- major source of free energy used by enzymes to lower the activation energy so increase the rate of a reaction
- gives enzyme its specificity for substrate
61
T/F enzymes are complementary to transition state, not substrate
true
62
what does the binding energy contributed by the formation of weak interactions between E and S is the transition state provide
much of the energy needed to lower activation energy
63
an enzyme lowers the free energy of activation for the reaction meaning,
the enzyme increases the reaction velocity
64
T/F an enzyme affects the overall free energy change and changes the equilibrium
false, is does not affect the overall free energy change, and does not change the equilibrium
65
an enzyme accelerates the approach to equilibrium by,
lowering free energy
G catalyzes < G uncatalyzed
66
substrate concentration
- typically get hyperbolic curves when plotting reaction rate versus substrate concentration
- cooperative/allosteric enzymes have a sigmoidal curve with respect to the level of substrate
67
Michaelis-Menten equation
Vo= (Vmax[S])/(Km+[S])
- describes rectangular hyperbola when velocity is plotted as function of substrate concentration
68
Km
- the substrate concentration giving half-maximal reaction velocity
- expressed in units of concentration (describes the affinity of enzyme for substrate)
small Km = high substrate affinity
high Km = low substrate aiffinity
69
enzymes that operate at their maximal rate _____ respond much to increases in [S] and can only respond to very large decreases [S]
cannot
70
Lineweaver-Burk
Linear plot
- Vmax is difficult to determine, requires very high [S]
71
enzyme inhibition
an inhibitor is a compound that interacts with an enzyme to slow the rate of an enzyme-catalyzed reaction
72
reversible inhibitors
bind to enzymes by noncovalent interactions
- enzyme activity recovers when inhibitor is removed
(enzyme with regain activity after inhibitor timeline)
73
example of reversible inhibitor
Ibuprofen and COX enzyme
74
irreversible inhibitors
inactivators react with enzymes through covalent bonds
- enzyme activity does not recover
75
example of irreversible inhibitor
aspirin (acetylsalicylic acid) and COX1
76
competitive reversible inhibitors
- binds reversibly in the active site
- inhibitor and substrate compete for access to enzyme
- statin drugs lower cholesterol by competing against HMG-CoA for the active site of HMG CoA reductase
- HMG-CoA is not converted to mevalonate >>>cholesterol
77
what is an inhibitor of HMG-CoA reductase
statins
78
competitive inhibitor effect on Km
increases the apparent Km for a substrate
- more substrate (higher Km) is needed to achieve 1/2 Vmax
79
competitive inhibitor effect on Vmax
not affected
- inhibition can be reversed by increasing [S]
80
non-competitive reversible inhibitors
- inhibitor binds reversibly to the enzyme, but at a different site than the substrate binding site
- inhibitors can bind to E and ES equally well
- changes Vmax but does not affect Km
81
example of non-competitive reversible inhibitor
cyanide blocks cytochrome C oxidase (complex IV in the ETC)
82
noncompetitive inhibitor effect on Vmax
lowers Vmax
- cannot be overcome by increasing substrate concentration
83
noncompetitive inhibitor effect on Km
no effect on substrate binding
- Hm does not change in the presence or absence of noncompetitive inhibitor
84
3 types of irreversible inhibitors
covalently modify an enzyme, destroying activity permanently
- group specific
- substrate analog
- suicide inhibitor
85
group specific irreversible inhibitor
forms covalent bond with specific aa side chain (whole inhibitor stays bound)
- Sarin gas inhibits acetylcholinesterase degrades neurotransmitter acetylcholine allowing muscle to relax after contraction
86
substrate analog irreversible inhibitor
looks like natural substrate, will react with enzyme and stay bound
87
suicide inhibitor irreversible inhibitor
unusual type, enzyme modifies the inhibitor into a reactive form in the active site
- aspirin (acetylsalicylic) acetylates Cox1 and salicylic acid leaves the pocket
88
allosteric regulation of enzyme activity
"another site"
- modulator homotropic effectors (substrate itself)
- modulator heterotropic effectors (downstream metabolite that feeds back to regulate the initial key step in pathway)
- allosteric agents induce shape changes in substrate pocket
89
allosteric regulation of enzyme activity of Vmax and Km
both can be affected
- enzymes often deviate from Michaelis-Menten kinetics
- activators can overcome accumulation of inhibitory factors
- inhibitors can prevent the waste of energy in making unnecessary products
90
catabolism
oxidation of carbon fuel
(breakdown of carbon molecules)
exergonic process
91
anabolism
energy consuming
reduction of carbon molecules
endergonic process
92
a high enthalpy and low entropy codes for a ______ free energy
higher
93
a low enthalpy and high entropy codes for a ____ free energy
lower
94
converging catabolism
- simplification -
many different sources are used to form acetate (acetyl-CoA)
95
diverging anabolism
- structural complexity -
acetate (acetyl-CoA) is used to start anabolism which forms many different products
96
cyclic pathway
- energy production -
biosynthetic intermediates (citrate and oxaloacetate in cycle with acetate)
97
favorable vs. non-favorable reaction in Gibbs free energy
favorable: exothermic
- equilibrium initial state
- reaches transition state
- releases energy to form product
- G is negative
non-favorable: endothermic
- initial state is 0
- energy consumed to reach transition state
- final state at equilibrium
- G is positive
98
T/F Delta G can only predict if a reaction will proceed spontaneously or not, cannot predict the kinetics or reaction rate
true
99
Delta G
change in free energy (ability of a reaction to do work)
100
Delta H
change in enthalpy (kind and number of chemical bonds)
101
Delta S
change in entropy (change in disorder or randomness)
102
glycolysis
1 glucose (6C) >>> 2 pyruvate (3C)
- steps 4, 5, 6 and 8 are unfavorable under standard condition WIHTOUT enzyme
- actual delta G near 0 (equilibrium) WITH enzyme
- metabolic flux
103
metabolic flux
influenced by the concentration of substrates and products
- high levels of substrates pushes reactions to the right to make products (competition for enzyme)
104
what is the delta G in erythrocytes during enzyme regulation
all reactions near equilibrium are reversible
- enzyme takes up the product for next steps and later taken away so it will not build up and the cycle can keep going
105
how do you carry out thermodynamically unfavorable reactions
couple them to other reactions that liberate free energy so that the overall process is exergonic (endergonic couples with exergonic)
106
standard free energies of hydrolysis
XDP ->
XTP ->
XTP ->
XDP -> XMP + Pi
XTP -> XDP + Pi
XTP -> XMP + PPi
107
UTP is used for
adding sugars
108
CTP is used for
lipid synthesis
109
GTP is used for
protein synthesis
110
what are the high energy metabolites in ATP
1,3-Bisphosoglycerate (glycolysis)
Phosphoenolpyruvate (glycolysis)
Creatine Phosphate (muscle)
Acetyl CoA (TCA cycle - binds to sulfur)
111
why is ATP called the cellular energy currency
- can be made from higher energy phosphates
- used as a phosphoryl group donor
- used to drive unfavorable reactions
112
how fast are TAP molecules consumed
60 seconds
113
how is ATP continually regenerated
via oxidation of carbon in fuel molecules like glucose, fast, proteins
114
what molecules are used for energy production
carbohydrates
lipids
proteins
115
energy utilization
60% of energy used for body warmth
- muscle contractions
- active ion transport
biosynthesis
116
what 3 factors of ATP play a key role
- electrostatic repulsion of negatively charged phosphate groups
- resonance stabilization of ADP and Pi
- stabilization of ADP and Pi due to hydration
117
difference between phosphoester bond and phosphoanhydride bond
phosphoester - attached to P and Rib
phosphoanhydride - in between each P with P bonded to negative O
118
electrostatic repulsion of ATP
- at pH 7, ATP carries 4 negative charges (ADP has 3)
- repulsion is reduced upon hydrolysis
119
what makes phosphorus more electrophilic in ATP
Mg2+ coordination (tendency to attract electrons)
120
resonance stabilization in ATP
- orthophosphate (Pi) has 4 forms
- ADP also better resonance than ATP
121
stabilization due to hydration in ATP
- water can bind more effectively to ADP and Pi, then it can bind to the phosphoanhydride portion of ATP
122
why is all cellular ATP not expended through simple hydrolysis
- lots of energy is released when ATP is hydrolyzed (ATP is kinetically stable because hydrolysis reaction has high Ea)
- fixable by an ATPase enzyme that grabs ATP and helps it get over the Ea barrier
123
what are the parts that make up the arginine finger
walker A (threonine)
walker B (aspartate)
glutamate (H bond)
alpha phosphate
beta phosphate
gamma phosphate
arginine finger
124
what parts of the arginine finger bond to Mg2+ and what is the job of Mg2+
walker A threonine and walker B aspartate
Mg2+ organizes and neutralizes as it reacts
125
walker A
threonine <-> serine
negatively charged to bond with Mg2+
126
walker B
aspartate <-> glutamate
negatively charged to bond with Mg2+
127
glutamate in the arginine finger
catalytic side chain that will interact with H20 and orient the oxygen to attack the gamma (Y) phophate
128
arginine finger subunit
long (+) side chain
interacts with negatively charged oxygen on gamma (Y) phosphate
129
besides walker A and B, what does Mg2+ bond to
Beta and Gamma phosphates
130
what is the end product of the arginine finger ATPase actvity
phosphate with OH group from H2O
131
what is H20 organized and deprotonated by in the arginine finger ATPase activity
glutamate (-OH becomes the nucleophile)
132
what is the only active form of ATPase
homomeric hexomere ring
133
what is the cycle that ATPase works in line with the arginine finger
- association of ligand (ATP) to enzyme binding pocket induces conformational change
- C and N domain close around ATP and now the surface only is able to react with incoming molecules
- gamma phosphate is released
- ADP product is released and the gamma phosphate can be transferred to another molecule
134
why do we not store all our energy as ATP
- many reactions are allosterically activated/inhibited by ATP levels
- making ATP is not a good choice as a molecule to store in large quantity reserve
135
what solves the problem as not storing all energy as ATP
muscle cells store high-energy phosphate bonds in the form of creatine phosphate
136
how fast is ATP used in the body
within seconds
137
phosphocreatine
storage of energy in muscle (P-creatine)
- replenishes ATP levels when standing ATP are used
- bridges gap between ATP hydrolysis and new ATP made from metabolism
creatine phosphate + ADP -> creatine + ATP
138
where is acetyl-CoA present
TCA cycle
139
from least reactive to most reactive, organize the different forms of acetyl-CoA
ester
thioester
acyl phosphate
140
why are thioester bonds higher in energy than ordinary esters
- 1 resonance form vs 2 resonance forms
- larger atomic size of S compared to O
- thioester is unstable relative to an ester; releases more energy on hydrolysis
141
steps in thioester adenylylation
- activate carboxyl (release pyrophosphate)
- 1 fatty acyl-CoA synthetase
- COA-SH 2 fatty acyl-CoA synthetase -- AMP released
- S-CoA (fatty acid oxidation)
142
activated carrier of acyl group and specific parts
- HS on B-mercaptoethylamine unit (REACTIVE GROUP)
- pantothenate unit (Vitamin B5)
- ADP
143
reduced (most energy) to oxidized (least energy) molecules
methane
methanol
formaldehyde
formic acid
carbon dioxide
144
no more oxygen can be added (e- poor)
oxidized
145
no more H+ can be added (e- rich)
reduced
146
what are the two main types of cellular fuels
glycolysis
beta oxidation
147
what are the 4 ways that there is a transfer of e- from donor to acceptor
- direct transfer
- as H atoms (H+ + e-)
(FAD -> FADH2) conjugate redox pair
- transferred as hydride ion
(2e-, occurs with NAD-linked dehydrogenases)
- direct combination with O2
(oxidation of hydrocarbon to alcohol)
148
how is most ATP made in the cell
oxidative phosphorylation
- transfer of e- from substrates to NAD+ [NADH] and FAD [FAD(2H)]
- to the mitochondrial ETC
- transfer of e- to oxygen
149
what are the two main carriers of electrons
NAD+ and FAD
150
plasma membrane:
components
barrier
interactions
organization
- lipids, proteins, sugars
- selective barrier
- cell-cell interactions through specific ligands/receptors
- compartmentalization of biochemical reactions (membranes permit the 2D organization/acceleration of reactions similar to 3D
151
transporters in the plasma membrane
allow the concentration (or exclusion) of compounds, and the establishment of electrical potentials
152
integral membrane proteins
traverse the lipid bilayer
- hydrophobic amino acids face the acyl chains of lipids
- hydrophilic C and N terminals face towards the extracellular area and cytoplasmic side
153
peripheral membrane proteins
can interact with other proteins or lipids
- lipid binding proteins have specific interactions through electrostatic interactions or amphipathic domain
- have an overall negative charge (electrostatic)
- not through the whole membrane
154
amphipathic domain
water loving amino acids stick out so they can interact with the membrane
155
how are integral and peripheral membrane proteins attached
anchored through a covalently attached lipid molecule
156
how are membrane proteins affected by lipid content
- proteins prefer rafts or thin membrane
- rafts are thicker membranes that cause high spikes
- tyrosine receptors are present on rafts
157
protein tilt
two proteins Criss cross as they are dragged though the domain (thick->thin)
- protein tilt facilitates information from one to the other
- hydrophobic mismatch and protein modifiers
158
membrane processes depend on what
- fluidity of the lipids
- determined by the fatty acid (FA) length and saturation
- cholesterol content (eukaryotes)
159
long saturated FA
- pack closely together
- stronger van der Walls interactions
- lower fluidity (butter solid at RT)
- long straight chains
160
unsaturated FA
(one or more cis double bonds)
- produces a bend in the hydrocarbon chain
- loose packing
- increases fluidity (veggie oil - liquid at RT)
161
cholesterol
- flat hydrophobic steroid core with a hydroxyl group at one end
- flexible hydrocarbon tail at other end
- interacts with acyl chains of other lipids
- STRONGER interactions with saturated FA
162
how do bacteria function even though they lack cholesterol
regulate the fluidity of their membranes by varying the number of double bonds and the length of their FA chain
- they have hopenoids (flattened lipids), which look similar
163
cylindrical membrane curvature
flat membrane
- phosphatidylcholine
- phosphatidylserine
164
conical membrane curvature
negative curvature (party hat)
- phosphatidylethanolamine
- phosphatidic acid
165
inverted-conical membrane curvature
positive curvature (ice cream cone)
- lyso-GPLs
- phosphoinositides
- ONE ACYL CHAIN
166
basic glycerophospholipid
- glycerol backbone (3 carbons and 3 OH)
- 2 --OH linked to FA through ester bond
- 3rd --OH linked to a phosphate (polar/hydrophilic head group) *fat storage*
- phosphate can be further linked to other molecules
167
phospholipase and types of PL
chop up phospholipids
- PLx
- PL (A1, A2, C, D)
x tells you where it cuts
168
PLD
phospholipase that acts on the distant glycerol
169
PLC
phospholipase that acts on the closer glycerol
170
PLA1
phospholipase responsible for acyl release on carbon 1
- chops ester bond on long chain
171
PLA2
phospholipase responsible for acyl release on carbon 2
172
what remains when PLA2 is activated and goes through hydrolysis
product is lysophospholipid (one tail)
separate fatty acid
173
types of glycerophospholipids
PC
PE
PS
PG
PI
phosphatidylcholine
phosphatidylethanolamine
phosphatidylserine
phosphatidylglycerol
phosphatidylinositol
174
T/F phospholipases are regulated
true
175
product after PLA1
leaves tail of carbon 2
176
product after PLA2
leaves tail on carbon 1
177
what does PLC specifically attack
PI 4,5-bisphosphate (PIP2)
178
how do lipids and many membrane proteins diffuse into the membrane
rapid lateral diffusion
- can be visualized using FRAP technique
179
T/F lateral diffusion of lipids is much more rapid than transverse diffusion (flip-flopping)
true
180
transverse movements of lipids
spontaneous (slow for GPL/SL and faster for Chol)
- protein lipid transporters help translocation
- can establish asymmetry or eliminates it
181
floppase
cytosol -> extracellular space/lumen
182
flippase
extracellular space/lumen -> cytosol
183
scramblases
remix through cytosol and extracellular space/lumen
184
what does lipid asymmetry do to promote the cell
- keeps PS on the inside, important because PS is a signal for cell damage and will lead to its destruction by white blood cells
- keeps signaling lipids on the inside, PS and PI variants interact with cytoplasmic proteins to carry out cellular functions (actin polymerization)
185
simple diffusion
- no proteins or energy
- nonpolar compounds only
- down concentration gradient
- O2 in : CO2 out
186
transport/facilitated diffusion
- down electrochemical gradient
- passive transport
- protein channel (high -> low concentration)
- glucose (GLUT 1/2/4)
187
why are transporters needed in a concentration gradient
during simple diffusion without transporter, there is a high energy barrier. The transporter will help lower the energy barrier allowing for concentration movement
188
simple diffusion vs facilitated diffusion Vmax
simple - no Vmax, no transporters
facilitated - Vmax and level out, occupy all transporter channels
189
primary active transport
- against electrochemical gradient
- hydrolyze ATP as energy source to move things against concentration gradients (swim upstream)
- P type ATPases
- V type ATPases
- ABC transporters
- ATP in : ADP + Pi out
190
secondary active transporters
- energy from primary transport (cargo going downstream) is used to move second cargo upstream (SYMPORTER)
- ANTPORTERS are similar but move cargo in opposite directions
- 2 molecules at once, high -> low, one going one way and one going the other
- SGLT1 (glucose in intestinal epithelial cells)
191
why must SGLT1 stay at high concentrations while GUT2 is low
must stay high to keep diffusion constant
192
three categories of chemical cell singaling
- cytoplasmic - direct, gap junctions
- cell to cell - contact mediated (MHCII - T cell receptor)
- free diffusion - one releases, one takes, distant or adjacent cells
193
what are the three stages of signal transduction
1- reception of extracellular signal by cell -> conformational shape change (each time ligand binds)
2- transduction of signal from outside of cell to inside of cell
3- cellular response - occurs entirely in the receiving cell
194
tyrosine kinase receptor
- growth factor
- 2 protein copies -> conformation change -> protein tilt between tyrosine kinase domains
- SH2 domain recognizes and binds phosphorylated tyrosine
195
protein kinases
use ATP and transfer a PO4 group to the OH group on a specific amino acid side chain (Tyr, Thr, Ser) of the target protein
- binding the ligand changes the shape of the intracellular kinase domain and activates domains
196
what are the three main amino acids that are phosphorylated in mammals
phosphoserine
phosphothreonine
phosphotyrosine
197
a protein that is activated by a protein kinase, in turn is inactivated by a ______
protein phosphate
(meaning effect of signals cannot last forever)
198
signal transduction steps by tyrosine kinase receptors
1- growth factors binding and dimerization
2- autophosphorylation
3- binding of adaptor proteins (Grb2)
4- complex assembly (binding of SOS (GEF) and Ras to Grb2) cascade of shape changes
5- guanine nucleotide exchange and activation of Ras (GDP also becomes GTP)
6- Ras binds raf and initiates MAP kinase pathway
199
what is Ras
small GTPase that is active when bound to GTP (binds to effector protein)
200
GEF (guanine exchange factor)
swaps out GDP for GTP to activate RAs in MAP kinase pathway
201
how does the MAP kinase pathway turn itself off
by hydrolyzing GTP to GDP with the help of a GAP (GTPase activating protein)
dysregulation -> uncontrolled cell growth -> cancer
202
steps in the signal transduction pathway by insulin receptors
1- insulin receptors autophosphorylze each other
2- binding of insulin response substrate (IRS)
3- IRS activates PI3 kinase - PI(4,5)P2 -> P3
4- PIP3 binds PH domains - protein kinases (PDK1 PKB)
203
what are G-protein coupled receptors
- hormone, cytokine or neurotransmitter binds to the receptor
- the activated receptor complex activates and acts as a GEF for the heterotrimeric G protein
GDP -> GTP
- GTP bound alpha separates and functions in downstream events (stimulates membrane bound enzymes leading to generation of second messengers)
204
what is the cellular response for the second messenger Gas
adenylyl cyclase - increase cAMP
205
what is the cellular response for the second messenger Ga i/o
inhibits adenylyl cyclase to increase cAMP
206
what is the cellular response for the second messenger Ga q/11
PLC-B
IP3/DAG/Ca2+
207
steps through the production of cAMP
1- Gas binds adenylyl cyclase (input of ATP)
2- second messenger (3',5'-cyclic AMP) activates protein kinase A (PKA)
3- cAMP phosphodiesterase activates PKA into 5'-AMP
208
steps through the production of IP3
1- signal molecule binds to the activated GCPR
2- activated Gq protein activates phospholipase C-B
3- PLC cleavage of [PI(4,5)P2] releasing diacylglycerol and phosphate
4- second messenger produced (IP3) in phosphate
5- activated protein kinase C from diacylglycerol
6- IP3 travels through the lumen of ER and through open IP3-gated Ca2+ release channel
7- second messenger (Ca2+) binds to activate protein kinase C
209
what are the inputs and the outputs of glycolysis
inputs:
- glucose molecule
- 2 ATP
- 2 NAD+
outputs:
- 2 pyruvate
- 4 ATP
- 2 NADH
210
T/F metabolic processes are compartmentalized in cells
true
211
where does glycolysis occur and for what cell types
in the cytoplasm in ALL cell types
212
how do cells without mitochondria (RBCs) get their energy production
they fully rely on glycolysis
213
what does the inability to carry out glycolysis result in
hemolytic anemia
214
what are the major carbohydrates in the human diet
- starch
- sucrose
- lactose
- fructose
- glucose
215
what first breaks down starch, lactose, and sucrose as it enters the stomach
salivary a-amylase
216
what breaks down carbohydrates further as it progresses from the stomach to the small intestine
a-dextrins from the stomach and a-amylase from the pancreas
217
starch definition and the forms
polymers of glucose
- linear a(1-4) bonds
- branch a(1-6) bonds - more prevalent in glycogen than in starch
218
starches being broken down by salivary a-amylase and pancreatic a-amylase, which both catalyze the hydrolysis of a(1-4) glycosidic bonds, produce...
a-maltose
a-isomaltose
tri/oligosaccharides
dextrins
(small intestine)
219
maltose
- disaccharide of glucose
- linked by an a(1-4) bond
- broken down by maltase
220
isomaltose
- disaccharide of glucose
- linked by an a(1-6) bond
- broken down by isomaltase
221
sucrose
- disaccharide of glucose linked to fructose
- linked in an a(1-2) linkage
- broken down by sucrase
222
sucrase-isomaltase complex deficiency
- results in an intolerance of ingested sucrose
- highly prevalent in the Inuit people
- treatment includes dietary restriction of sucrose, and enzyme replacement therapy
223
lactose
- disaccharide of galactose + glucose
- linked by a B(1-4) linkage
- broken down by lactase
224
absence of lactase and treatment options
- lactose intolerance affects more than 75% of the world's adults
- treatment is to reduce the consumption of milk
225
intestinal glucose-fructose absorption through the SGLT1/GLUT 2 Pathway
what is SGLT1 and what does it do
(sodium-glucose linked transporter 1)
- symporter: transports glucose + galactose against a concentration gradient (low to high)
- energy provided by an electrochemical gradient of sodium (high to low)
- present on apical border of intestinal cells
226
intestinal glucose-fructose absorption through the SGLT1/GLUT 2 Pathway
what is Na+/K+ and what does it do
- antiporter: uses ATP to move NA+ from low to high levels
- keeps cytoplasmic levels low -> helps continued SGLT1 operation
227
symporter vs antiporter
symporter - transports 2 different molecules in the same direction
antiporter - transports 2 different molecules in the opposite direction
228
intestinal glucose-fructose absorption through the SGLT1/GLUT 2 Pathway
what is GLUT2 and what does it do
- facilitated glucose transporter
- transports glucose down its concentration gradient (high to low)
- on basolateral side
- high capacity (Vmax) but low affinity (high Km) for glucose -> will move high glucose quickly
229
intestinal glucose-fructose absorption through the SGLT1/GLUT 2 Pathway
what is GLUT5 and what does it do
- facilitated fructose transporter
- on apical border
- separate from the rest of the system
230
why does the NA+/K+ pump use ATP
hydrolyzing ATP will help the flow
231
what does SGLT1 deficiency cause
glucose and galactose malabsorption
232
what does GLUT5 deficiency cause
fructose malabsorption (dietary fructose intolerance)
233
investment stage of glycolysis steps 1-3
1: glucose --> glucose 6-phosphate (hexokinase phosphorylation - ATP to ADP)
2: glucose 6-phosphate to fructose 6-phosphate
(phosphoglucoseisomerase - isomerization)
3: fructose 6-phosphate to fructose 1,6-biphosphate
(phosphofructokinase phosphorylation - ATP to ADP)
234
payoff stage of glycolysis steps 4-10
4: fructose 1,6-biphosphate to dihydroxyacetone phosphate OR glyceraldehyde 3-phosphate
(aldolase)
5: dihydroxyacetone to glyceraldehyde 3-phosphate
(triosephosphate isomerase)
6: glyceraldehyde 3-phosphate to 1,3-biphosphoglycerate
(glyceraldehyde phosphate dehydrogenase - NAD+ to NADH)
7: 1,3-biphosphoglycerate to 3-phosphoglycerate
(phosphoglycerate kinase - ADP to ATP)
8: 3-phosphoglycerate to 2-phosphoglycerate
(phosphoglycerate mutase - change shape)
9: 2-phosphoglycerate to phosphoenolpyruvate
(enolase)
10: phosphoenolpyruvate to pyruvate
(pyruvate kinase - ADP to ATP)
235
what are the two steps in glycolysis where ATP is generated and by what enzymes
steps 7 and 10 of the payoff phase
7: phosphoglycerate kinase
10: pyruvate kinase
236
energy investment phase of glycolysis purpose
- uses 2 molecules of ATP/glucose but makes no ATP
- traps and prepares glucose for oxidation steps
237
what are the five steps on how glucose is converted into glyceraldehyde 3-phosphate (GAP) in glycolysis
1- phosphorylation of glucose
2- isomerization
3- second phosphorylation of fructose 6P (committed step)
4- cleavage into two 3-carbon molceules
5- isomerization of DHAP to GAP
238
glycolysis step 1: phosphorylation
phosphoryl group:
- traps glucose inside the cell
- acts as handle for enzyme recognition and provides increased binding free energy
- glucose bonds FIRST
- cleft closing dehydrates active site; prevents nucleophilic attack by water and nonproductive ATPase
- nonpolar binding site excludes water to favor reaction (facilitates aspartate to act as base and start reaction)
OH is activated into (OPO3)2- by hexokinase with the use of 1 ATP
glucose -> glucose 6P
239
hexokinase reaction (phosphoryl group transfer) key steps
- the C6 (OH) must be deprotonated to act as nucleophile
- aspartate (base) is catalytic pocket deprotonates C6 (OH) -> becomes aspartic acid
- charged C6 (O-) attacks gamma Phosphate
- covalent bond (intermediate) between C6 (O) and P
- phosphoanyhdride bond between beta and gamma phosphates is broken
- ADP becomes the good leaving group and dettaches
240
regulation of glucose phosphorylation key steps of hexokinase 1 as regulatory step and feedback inhibited; hexokinase IV
hexokinase 1: irreversible but regulatory step
- excess of glucose 6P in allosteric pockets
- has a LOW Km and lower Vmax (lower capacity)
- permits efficient phosphorylation of glucose even at low concentrations
hexokinase 1: feedback inhibited by glucose 6P
- prevents it from tying up all the intracellular Pi in the form of G-6-P
hexokinase IV (glucokinase):
- expressed in hepatocytes (liver) and pancreatic b cells
- high Km and Vmax (increased capacity)
- not inhibited by G-6-P
241
Km and Vmax of glucokinase and hexokinase during regulation of glucose phosphorylation
Km: glucokinase>hexokinase
spare glucose for brain, muscle and other tissues
- higher concentration: glycogen storage
Vmax: glucokinase>hexokinase
at fasting glc concentration, hexokinase is at Vmax, glucokinase activity varies according to glc concentration
- hexokinase low due to negative feedback of G6P
242
glycolysis step 2: isomerization
conversion of an aldose to a ketose sugar
- reversible + dependent on metabolic flux
- goal is to convert the 6C starting material into 2x 3C units
- carbonyl at C1 is in "wrong" spot for cleavage by aldol reaction
- isomerization moves carbonyl to C2 to promote reaction
243
glycolysis step 2: isomerization pathway steps
1: G-6P <-> open ring (aldehyde)
2: aldehyde <-> ketone (phosphoglucose isomerase)
3: ketone <-> F-6P (closure at C2)
244
phosphoglucose isomerase: mechanism
1- base deprotonates H20 -> :OH
2- lys organizes :OH-
3- OH- deprotonates C1-OH -> H2O
4- C5-O deprotonates His
5- ring opens
6- glutamate deprotonates C2-H -> enediolate (2 alcohols not stable)
7- enediolate deprotonates glutamic acid -> ketone
8- HIS deprotonates C5-OH
9- ring closes -> F-6P
245
glycolysis step 3: second phosphorylation key steps
F-6P to F-1,6BP by phosphofructokinase (ATP IS USED)
- committed step (irreversible)
- cell can now split fructose 1,6-BP into two trioses
- better to have a phosphoryl group at each end of fructose so that the resulting trioses are both phosphorylated
- allosterically regulated by ATP, AMP, etc
- MOST IMPORTANT regulatory point in glycolysis
246
what allows the transition from F-6P + ATP to F-1,6BP + ADP
- AMP
- ADP
- F-2,6BP
247
what inhibits the transition from F-6P + ATP to F-1,6BP + ADP
- ATP
- citrate
248
what is PFK-1 allosterically inhibited by
ATP, which acts as an energy rich signal
(abundance of ATP will bind and weaken PFK-1)
249
during the regulation of phosphofructokinase1, where does ATP bind
the 2nd site away from catalytic site
(when in excess/park of feedback)
- AKA: allosteric inhibitor
250
why does AMP reverse inhibition by ATP during the regulation of phosphofructokinase
PFK-1 is very sensitive to AMP regulation
251
what does the enzyme aldolase split F-1,6BP in to
dihydroxyacetone phosphate (DHAP)
glyceraldehyde 3-phosphate (GAP)
although this reaction is energetically uphill, the products are rapidly depleted, pulling the reaction forward
252
glycolysis step 5: isomerization of DHAP and G3-P
DHAP <-> G3-P
reversible by triose phosphate isomerase
- end of energy investment stage
- ketose-aldose isomerase (goes through enol intermediate as seen before)
- isomerization produces 2 molecules of G3-P from the cleavage of F-1,6BP
- continual metabolism of G3-P in glycolysis drives the reaction forward
253
second stage of glycolysis overview
2 X 3-carbon units are oxidized to pyruvate
- generating 4 molecules of ATP and 2 NADH
254
what are the 5 steps on how glyceraldehyde 3P is converted to pyruvate
6. oxidation of G3-P to 1,3-BPG
7. phosphorylation of ADP
8. mutase: conversion of 3-PG to 2-PG
9. dehydration by enolase
10. phosphorylation of ADP, giving pyruvate
254
glycolysis step 6: oxidation of glyceraldehyde 3-P key notes
DOES NOT USE ATP
- oxidation of GAP powers the formation of 1,3-biphosphoglycerate, which has a high phosphoryl transfer potential
- 1,3-biphosphoglycerate is acyl phosphate, which is mixed anhydride of phosphoric acid and a carboxylic acid
done by a dehydrogenase
255
is aldehyde to carboxylic acid through oxidation favorable or unfavorable
favorable
256
is aldehyde to carboxylic acid through dehydration favorable or unfavorable
unfavorable
257
coupling of the two processes of acyl-phosphate formation (by GADPH) allows the conservation of energy released by oxidation without thioester intermediate
large delta G = unfavorable
- reaction of stable carboxylate with phosphate
258
coupling of the two processes of acyl-phosphate formation (by GADPH) allows the conservation of energy released by oxidation with thioester intermediate
energy is trapped in thioester
(starts to level out to equilibrium)
259
lys219 in the phosphoglycerate kinase step guides C1-P where
to gamma position of ATP
(substrate level phosphorylation)
260
glycolysis step 8: shift of the phosphate group from C3 to C2
done by phosphoglycerate mutase
- around equilibrium delta G
261
allosteric shape change during phosphoglycerate mutase
substrate shift
- His deprotonates C2-OH to attack Phospho-His
- C2-O- oxyanion gets Pi from Phospho-His to 2,3 biphosphoglycerate
- dephosphorylated His takes Pi from C3-Pi to 2 phosphoglycerate
(RXN uses 2 separate phosphates)
262
glycolysis step 9: dehydration of 2-phosphoglycerate
enolase converts 2-phosphoglycerate into phosphoenolpyruvate (alkene)
- high phosphoryl group transfer potential
263
step 10 glycolysis: pyruvate kinase and regulators
- ATP generation step - substrate level phosphorylation
- reaction is irreversible and regulated
regulators:
- allosteric activator: F-1,6BP
- allosteric inhibitor: ATP
- protein phosphorylation
264
aerobic vs anaerobic glycolysis
total (NAD+ + NADH) is very low relative to amount of glucose metabolized in a few minutes
aerobic:
- reducing power of NADH is transferred to mitochondria by the malate-aspartate and glycerol 3-phosphate shuttles, regenerating NAD+
- 30-32 ATPs/glucose are produced
anaerobic:
- NADH oxidized to NAD+ by lactate dehydrogenase
- 2 ATPs/glucose are produced
265
what is the role of alcohol dehydrogenase
convert glyceraldehyde to glycerol which further produces glycerol-P and triglycerides
266
glycogen
short term storage
267
glycogen granule structure
- y particles are protein rich subunits of 3nm wide
268
alpha granule structure
liver - slow
- composed of several B-granules bound via a protein backbone rich in disulfide bonds
269
beta-granule structure
muscle - fast
- includes the carbohydrate polymer and the bound y-particles
270
what is the role of glycogenin (GN) in the glycogen granule formation intermolecularly and intramolecularly
Dimer (weak binding)
- intermolecular glycosylation (transfer of 1-2 glucose to Tyr-194 from partner GN)
- intramolecular glycosylation (elongation of primer chain)
271
what is the role of glycogen synthase (GS) in the glycogen granule formation
elongation of the primer chain through a-1,4 linkage
- displaces one of the GN dimer copies
272
what is the role of the glycogen-branching enzyme (GBE) in the glycogen granule formation
adds glucose residues to the granule through a-1,6 linkage
273
in glycogen granule formation, GN binds to _____ for the start of glycogen synthesis
actin filaments
274
what are actin filaments
used for cytoskeleton mobility
275
how many later can beta granules have
up to 12
- number of glucose double with each layer
- a 13th layer is impossible due to spatial constraints
276
what is glycogen so highly branched
- makes it more soluble
- allows for much faster synthesis/degradation
- good for flight or fight response
277
what are the 4 components of glycogen structure
- glucose residue linked a-1,4 (every 8-10)
- glucose residue linked a-1,6
- reducing end attaching to glycogenin
- nonreducing ends
278
what are the 6 steps to glycogenesis
1- glucokinase (hexokinase 4) - phosphorylate
2- phosphoglucomutase - glycogen production
3- UDP-glucose phosphorylase - create good LG
4- glycogenin (GN) - grows chain
5- glycogen synthase (GS)
6- glycogen branching enzyme (GBE)
279
phosphoglucomutase simple reaction
glucose-1P <-> intermediate <-> glucose-6P
phosphate gets moved around to different carbons
280
5 steps of phosphoglucomutase
1- C1-OH must be deprotonated by enzyme (going backwards starting at 4)
2- negative CO- will attack PO4 on Ser
3- Ser-OH is protonated by enzyme BH
4- Ser-OH is deprotonated
5- Ser-O- will attack PO4 on glucose
281
in phosphoglucomutase, why must we convert Glucose-1P to Glucose-6P
it must be switched to enter glycolysis
282
T/F phosphoglucomutase and glycogen phosphorylase use ATP
false, neither of them do
283
how many ATPs do we get per glucose via glycolysis when starting with glycogen
3
284
what is the committed step (activation of glucose) in glycogenolysis
- UDP-glucose is the donor of glucose in the formation of glycogen
- spontaneous hydrolysis of the -P bond in PPI drive the overall reaction
- cleavage of PPI is the only energy cost for glycogen synthesis
- glycogen synthase promotes the transfer of the glucosyl residue from UDP-glucose to a non-reducing end of the branched glycogen molecule
285
what is glycogenin
- protein homodimer with a MW of 37 kDa
- functions as a primer
- AUTOGLUCOSYLATES at a specific Tyr-194
- acts as glucosyltransferase
- forms a tight 1:1 complex with glycogen synthase
286
what enzyme is used in glycogenolysis and what does it do
glycogen phosphorylase
- catalyzes the phosphorylsis (not hydrolysis) of glucose units from glycogen (cuts off 1 each time until there are no more)
- inorganic phosphate in the nucleophile
- releases them as glucose-1P
- DOES NOT USE ATP
- energy of the glycosidic bond is captured in the sugar phosphate
287
3 enzyme steps of glycogenolysis
1- phosphorylase: release of glucose-1P
2- transferase: remodeling of the glycogen to allow further degradation -> 3 residues from branch get moved to the end of a chain
3- a-1,6 glucosidase removes branch point residue
steps 2 and 3 are performed by the same debranching enzyme
288
in glycogenolysis, linked 1-1,4 dimers cannot be removed and put back on to the end of a chain without what two enzymes
glycogen phosphorylase
limit dextrin
289
glycogenolysis in the muscle
glycolysis is used to break glucose-6P down into energy
- no release into blood
290
glycogenolysis in the liver
glucose-6P is used to generate free glucose which can be shunted to other tissue for use
- controls blood-glucose levels (high-low)
291
what are the 3 fates of glucose-6P
1- it is the initial substrate for glycolysis
2- it can be processed by the pentose phosphate pathway to yield NADPH and ribose derivatives
3- it can be converted into free glucose for release into the bloodstream
292
regulation of glycogen synthesis in the liver
ALLOSTERIC
glucose-1P -> glucose-6P by glycogen synthase promotes glycogen
glycogen -> glucose-1P by glycogen phosphorylase is inhibited by glucose-6P, ATP, and glucose
glucose-1P does not need to be regenerated
293
glycogenolysis in the liver key points: role of epinephrine and glucagon
- driven mostly by glucagon but also requires epinephrine signaling
- glucagon from alpha cells in pancreas
- epinephrine from adrenal glands and neurons - bonds adrenergic receptors
294
regulation of glycogen synthesis and degradation in muscle
ALLOSTERIC
glucose-1P -> glucose-6P by glycogen synthase promotes glycogen
glycogen -> glucose-1P by glycogen phosphorylase is inhibited by glucose-6P, ATP, BUT promoted by AMP
295
MCB 450
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